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ORCIDNucleic Acids Research, Volume 45
Volume 45, Number Database-Issue, January 2017
- Michael Y. Galperin
, Xosé M. Fernández-Suárez, Daniel J. Rigden:
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. D1-D11 - Database Resources of the National Center for Biotechnology Information. D12-D17
- The BIG Data Center: from deposition to integration to translation. D18-D24
- Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi:
DNA Data Bank of Japan. D25-D31 - Ana Luisa Toribio, Blaise T. F. Alako, Clara Amid, Ana Cerdeño-Tárraga, Laura Clarke, Iain Cleland, Susan Fairley, Richard Gibson, Neil Goodgame, Petra ten Hoopen, Suran Jayathilaka, Simon Kay, Rasko Leinonen, Xin Liu, Josué Martínez-Villacorta, Nima Pakseresht, Jeena Rajan, Kethi Reddy, Marc Rossello, Nicole Silvester, Dimitriy Smirnov, Daniel Vaughan, Vadim Zalunin, Guy Cochrane:
European Nucleotide Archive in 2016. D32-D36 - Dennis A. Benson, Mark Cavanaugh, Karen Clark, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, Eric W. Sayers:
GenBank. D37-D42 - Keren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu:
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. D43-D50 - René Dreos, Giovanna Ambrosini, Romain Groux, Rouaïda Cavin Périer, Philipp Bucher:
The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms. D51-D55 - Fabrice P. A. David, Jacques Rougemont, Bart Deplancke:
GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms. D56-D60 - Ivan S. Yevshin, Ruslan N. Sharipov, Tagir F. Valeev, Alexander E. Kel, Fedor A. Kolpakov:
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. D61-D67 - Tobias Penzkofer, Marten Jäger, Marek Figlerowicz, Richard Badge, Stefan Mundlos, Peter N. Robinson, Tomasz Zemojtel:
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. D68-D73 - Shangwei Ning, Ming Yue, Peng Wang, Yue Liu, Hui Zhi, Yan Zhang, Jizhou Zhang, Yue Gao, Maoni Guo, Dianshuang Zhou, Xin Li, Xia Li:
LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs. D74-D78 - Jing Gong, Chun-Jie Liu, Wei Liu, Yu Xiang, Lixia Diao, An-Yuan Guo, Leng Han:
LNCediting: a database for functional effects of RNA editing in lncRNAs. D79-D84 - Pohao Ye, Yizhao Luan, Kaining Chen, Yizhi Liu, Chuanle Xiao, Zhi Xie:
MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing. D85-D89 - Christina Backes, Tim Kehl, Daniel Stöckel, Tobias Fehlmann, Lara Schneider, Eckart Meese, Hans-Peter Lenhof, Andreas Keller:
miRPathDB: a new dictionary on microRNAs and target pathways. D90-D96 - Ricardo Lebrón, Cristina Gómez-Martín, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Michael Hackenberg, José L. Oliver:
NGSmethDB 2017: enhanced methylomes and differential methylation. D97-D103 - Boqin Hu, Yu-Cheng T. Yang, Yiming Huang, Yumin Zhu, Zhi John Lu:
POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. D104-D114 - Ying Yi, Yue Zhao, Chunhua Li, Lin Zhang, Huiying Huang, Yana Li, Lanlan Liu, Ping Hou, Tianyu Cui, Puwen Tan, Yongfei Hu, Ting Zhang, Yan Huang, Xiaobo Li, Jia Yu, Dong Wang:
RAID v2.0: an updated resource of RNA-associated interactions across organisms. D115-D118 - Piroon Jenjaroenpun, Thidathip Wongsurawat, Sawannee Sutheeworapong, Vladimir A. Kuznetsov:
R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops. D119-D127 - The RNAcentral Consortium:
RNAcentral: a comprehensive database of non-coding RNA sequences. D128-D134 - Ting Zhang, Puwen Tan, Liqiang Wang, Nana Jin, Yana Li, Lin Zhang, Huan Yang, Zhenyu Hu, Lining Zhang, Chunyu Hu, Chunhua Li, Kun Qian, Changjian Zhang, Yan Huang, Kongning Li, Hao Lin, Dong Wang:
RNALocate: a resource for RNA subcellular localizations. D135-D138 - Sunil Kumar, Giovanna Ambrosini, Philipp Bucher:
SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity. D139-D144 - Sebastian Schmeier, Tanvir Alam, Magbubah Essack, Vladimir B. Bajic:
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions. D145-D150 - Dongsheng Chen, Sanjie Jiang, Xiaoyan Ma, Fang Li:
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species. D151-D157
- The UniProt Consortium:
UniProt: the universal protein knowledgebase. D158-D169 - Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria Jesus Martin, Johannes Söding, Martin Steinegger:
Uniclust databases of clustered and deeply annotated protein sequences and alignments. D170-D176 - Pascale Gaudet, Pierre-André Michel, Monique Zahn-Zabal, Aurore Britan, Isabelle Cusin, Marcin Domagalski, Paula Duek Roggli, Alain Gateau, Anne Gleizes, Valérie Hinard, Valentine Rech de Laval, JinJin Lin, Frédéric Nikitin, Mathieu Schaeffer, Daniel Dinis Teixeira, Lydie Lane, Amos Bairoch:
The neXtProt knowledgebase on human proteins: 2017 update. D177-D182 - Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D. Thomas:
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. D183-D189 - Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Young Mi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell:
InterPro in 2017 - beyond protein family and domain annotations. D190-D199 - Aron Marchler-Bauer, Bo Yu, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Fu Lu, Gabriele H. Marchler, James S. Song, Narmada Thanki, Zhouxi Wang, Roxanne A. Yamashita, Dachuan Zhang, Chanjuan Zheng, Lewis Y. Geer, Stephen H. Bryant:
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. D200-D203 - Christina A. Vivelo, Ricky Wat, Charul Agrawal, Hui Yi Tee, Anthony Kar Lun Leung:
ADPriboDB: The database of ADP-ribosylated proteins. D204-D209 - David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin:
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation. D210-D218 - Damiano Piovesan, Francesco Tabaro, Ivan Micetic, Marco Necci, Federica Quaglia, Christopher J. Oldfield, Maria Cristina Aspromonte, Norman E. Davey, Radoslav Davidovic, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V. Kajava, Lajos Kalmár, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B. Roche, Edoardo Salladini, Éva Schád, Antoine Schramm, Beáta Szabó, Ágnes Tantos, Fiorella Tonello, Konstantinos D. Tsirigos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Per Warholm, Vladimir N. Uversky, A. Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C. E. Tosatto:
DisProt 7.0: a major update of the database of disordered proteins. D219-D227 - Márton Miskei, Csaba Antal, Mónika Fuxreiter:
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies. D228-D235 - Hugues Ripoche, Elodie Laine, Nicoletta Ceres, Alessandra Carbone:
JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures. D236-D242 - Pawel Dabrowski-Tumanski, Aleksandra I. Jarmolinska, Wanda Niemyska, Eric J. Rawdon, Kenneth C. Millett, Joanna I. Sulkowska:
LinkProt: a database collecting information about biological links. D243-D249 - Andrei L. Lomize, Mikhail A. Lomize, Shean R. Krolicki, Irina D. Pogozheva:
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. D250-D255 - Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao:
mutLBSgeneDB: mutated ligand binding site gene DataBase. D256-D263 - Yang Xu, Shuang Zhang, Shaofeng Lin, Yaping Guo, Wankun Deng, Ying Zhang, Yu Xue:
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. D264-D270 - Peter W. Rose, Andreas Prlic, Ali Altunkaya, Chunxiao Bi, Anthony R. Bradley, Cole H. Christie, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Rachel Kramer Green, David S. Goodsell, Brian P. Hudson, Tara Kalro, Robert Lowe, Ezra Peisach, Christopher Randle, Alexander S. Rose, Chenghua Shao, Yi-Ping Tao, Yana Valasatava, Maria Voigt, John D. Westbrook, Jesse Woo, Huanwang Yang, Jasmine Young, Christine Zardecki, Helen M. Berman, Stephen K. Burley:
The RCSB protein data bank: integrative view of protein, gene and 3D structural information. D271-D281 - Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura:
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. D282-D288 - Natalie L. Dawson, Tony E. Lewis, Sayoni Das, Jonathan G. Lees, David A. Lee, Paul Ashford, Christine A. Orengo, Ian Sillitoe:
CATH: an expanded resource to predict protein function through structure and sequence. D289-D295 - R. Dustin Schaeffer, Yuxing Liao, Hua Cheng, Nick V. Grishin:
ECOD: new developments in the evolutionary classification of domains. D296-D302 - Lee Whitmore, Andrew John Miles, Lazaros Mavridis, Robert W. Janes, B. A. Wallace:
PCDDB: new developments at the Protein Circular Dichroism Data Bank. D303-D307 - Lisanna Paladin, Layla Hirsh, Damiano Piovesan, Miguel A. Andrade-Navarro, Andrey V. Kajava, Silvio C. E. Tosatto:
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. D308-D312 - Stefan Bienert, Andrew Waterhouse, Tjaart A. P. de Beer, Gerardo Tauriello, Gabriel Studer, Lorenza Bordoli, Torsten Schwede:
The SWISS-MODEL Repository - new features and functionality. D313-D319 - Liam D. H. Elbourne, Sasha G. Tetu, Karl A. Hassan, Ian T. Paulsen:
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. D320-D324 - Julia Varga, László Dobson, István Reményi, Gábor E. Tusnády:
TSTMP: target selection for structural genomics of human transmembrane proteins. D325-D330 - The Gene Ontology Consortium:
Expansion of the Gene Ontology knowledgebase and resources. D331-D338 - Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan P. Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman Elsayed, Cathy H. Wu:
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. D339-D346 - Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He:
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. D347-D352
- Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima:
KEGG: new perspectives on genomes, pathways, diseases and drugs. D353-D361 - Damian Szklarczyk, John H. Morris, Helen Cook, Michael Kuhn, Stefan Wyder, Milan Simonovic, Alberto Santos, Nadezhda T. Doncheva, Alexander Roth, Peer Bork, Lars Juhl Jensen, Christian von Mering:
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. D362-D368 - Andrew Chatr-aryamontri, Rose Oughtred, Lorrie Boucher, Jennifer M. Rust, Christie S. Chang, Nadine Kolas, Lara O'Donnell, Sara Oster, Chandra L. Theesfeld, Adnane Sellam, Chris Stark, Bobby-Joe Breitkreutz, Kara Dolinski, Mike Tyers:
The BioGRID interaction database: 2017 update. D369-D379 - Sandra Placzek, Ida Schomburg, Antje Chang, Lisa Jeske, Marcus Ulbrich, Jana Tillack, Dietmar Schomburg:
BRENDA in 2017: new perspectives and new tools in BRENDA. D380-D388 - Sunmo Yang, Chan Yeong Kim, Sohyun Hwang, Eiru Kim, Hyojin Kim, Hongseok Shim, Insuk Lee:
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH). D389-D396 - Shujing Li, Ke Shui, Ying Zhang, Yongqiang Lv, Wankun Deng, Shahid Ullah, Luoying Zhang, Yu Xue:
CGDB: a database of circadian genes in eukaryotes. D397-D403 - Katherine Wolstencroft, Olga Krebs, Jacky L. Snoep, Natalie J. Stanford, Finn Bacall, Martin Golebiewski, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, David D. van Niekerk, Alan R. Williams, Lars Malmström, Bernd Rinn, Wolfgang Müller, Carole A. Goble:
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. D404-D407 - Gregorio Alanis-Lobato, Miguel A. Andrade-Navarro, Martin H. Schaefer:
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. D408-D414 - Anne Morgat, Thierry Lombardot, Kristian B. Axelsen, Lucila Aimo, Anne Niknejad, Nevila Hyka-Nouspikel, Elisabeth Coudert, Monica Pozzato, Marco Pagni, Sébastien Moretti, Steven Rosanoff, Joseph Onwubiko, Lydie Bougueleret, Ioannis Xenarios, Nicole Redaschi, Alan J. Bridge:
Updates in Rhea - an expert curated resource of biochemical reactions. D415-D418 - Sara Rahmati, Mark Abovsky, Chiara Pastrello, Igor Jurisica:
pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis. D419-D426 - Omer Basha, Ruth Barshir, Moran Sharon, Eugene Lerman, Binyamin F. Kirson, Idan Hekselman, Esti Yeger Lotem:
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues. D427-D431 - Sarah A. Sam, Joelle Teel, Allison N. Tegge, Aditya Bharadwaj, T. M. Murali:
XTalkDB: a database of signaling pathway crosstalk. D432-D439 - Miguel Ramirez-Gaona, Ana Marcu, Allison Pon, An Chi Guo, Tanvir Sajed, Noah A. Wishart, Naama Karu, Yannick Djoumbou Feunang, David Arndt, David S. Wishart:
YMDB 2.0: a significantly expanded version of the yeast metabolome database. D440-D445
- Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Olena Verezemska, Michelle Isbandi, Alex D. Thomas, Rida Ali, Kaushal Sharma, Nikos Kyrpides, T. B. K. Reddy:
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements. D446-D456 - David Páez-Espino, I-Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Ernest Szeto, Manoj Pillay, Jinghua Huang, Victor M. Markowitz, Torben Nielsen, Marcel Huntemann, T. B. K. Reddy, Georgios A. Pavlopoulos, Matthew B. Sullivan, Barbara J. Campbell, Feng Chen, Katherine D. McMahon, Steven J. Hallam, Vincent J. Denef, Ricardo Cavicchioli, Sean M. Caffrey, Wolfgang R. Streit, John Webster, Kim M. Handley, Ghasem H. Salekdeh, Nicolas Tsesmetzis, João C. Setubal, Phillip B. Pope, Wen-Tso Liu, Adam R. Rivers, Natalia Ivanova, Nikos Kyrpides:
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. D457-D465 - Yun Zhang, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, Sanjeev Kumar, Christopher N. Larsen, Alexandra J. Lee, Xiaomei Li, Catherine Macken, Colin Mahaffey, Brett E. Pickett, Brian Reardon, Thomas Smith, Lucy Stewart, Christian Suloway, Guangyu Sun, Lei Tong, Amy L. Vincent, Bryan Walters, Sam Zaremba, Hongtao Zhao, Liwei Zhou, Christian M. Zmasek, Edward B. Klem, Richard H. Scheuermann:
Influenza Research Database: An integrated bioinformatics resource for influenza virus research. D466-D474 - Hyerin Kim, NaNa Kang, Kyuhyeon An, Doyun Kim, Jae Hyung Koo, Min-Soo Kim:
MRPrimerV: a database of PCR primers for RNA virus detection. D475-D481 - Eneida Hatcher, Sergey A. Zhdanov, Yiming Bao, Olga Blinkova, Eric P. Nawrocki, Yuri Ostapchuck, Alejandro A. Schäffer, J. Rodney Brister:
Virus Variation Resource - improved response to emergent viral outbreaks. D482-D490 - Ana Laura Grazziotin, Eugene V. Koonin, David M. Kristensen:
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. D491-D498 - Koenraad Van Doorslaer, Zhiwen Li, Sandhya Xirasagar, Piet Maes, David Kaminsky, David Liou, Qiang Sun, Ramandeep Kaur, Yentram Huyen, Alison A. McBride:
The Papillomavirus Episteme: a major update to the papillomavirus sequence database. D499-D506 - I-Min A. Chen, Victor M. Markowitz, Ken Chu, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Evan Andersen, Marcel Huntemann, Neha Varghese, Michalis Hadjithomas, Kristin Tennessen, Torben Nielsen, Natalia Ivanova, Nikos Kyrpides:
IMG/M: integrated genome and metagenome comparative data analysis system. D507-D516 - David Vallenet, Alexandra Calteau, Stéphane Cruveiller, Mathieu Gachet, Aurélie Lajus, Adrien Josso, Jonathan Mercier, Alexandre Renaux, Johan Rollin, Zoé Rouy, David Roche, Claude Scarpelli, Claudine Médigue:
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. D517-D528 - Daniel R. Mende, Ivica Letunic, Jaime Huerta-Cepas, Simone S. Li, Kristoffer Forslund, Shinichi Sunagawa, Peer Bork:
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. D529-D534 - Alice R. Wattam, James J. Davis, Rida Assaf, Sébastien Boisvert, Thomas S. Brettin, Christopher Bun, Neal Conrad, Emily M. Dietrich, Terry Disz, Joseph L. Gabbard, Svetlana Gerdes, Christopher S. Henry, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Eric K. Nordberg, Gary J. Olsen, Daniel E. Murphy-Olson, Robert Olson, Ross A. Overbeek, Bruce D. Parrello, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Andrew S. Warren, Fangfang Xia, Hyun Seung Yoo, Rick L. Stevens:
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. D535-D542 - Ingrid M. Keseler, Amanda Mackie, Alberto Santos-Zavaleta, Richard Billington, César Bonavides-Martínez, Ron Caspi, Carol A. Fulcher, Socorro Gama-Castro, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Luis Muñiz-Rascado, Quang Ong, Suzanne M. Paley, Martín Peralta-Gil, Pallavi Subhraveti, David A. Velázquez-Ramírez, Daniel S. Weaver, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp:
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12. D543-D550 - Takatomo Fujisawa, Rei Narikawa, Shin-ichi Maeda, Satoru Watanabe, Yu Kanesaki, Koichi Kobayashi, Jiro Nomata, Mitsumasa Hanaoka, Mai Watanabe, Shigeki Ehira, Eiji Suzuki, Koichiro Awai, Yasukazu Nakamura:
CyanoBase: a large-scale update on its 20th anniversary. D551-D554 - Kai Blin, Marnix H. Medema, Renzo Kottmann, Sang Yup Lee, Tilmann Weber:
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters. D555-D559 - Michalis Hadjithomas, I-Min A. Chen, Ken Chu, Jinghua Huang, Anna Ratner, Krishna Palaniappan, Evan Andersen, Victor M. Markowitz, Nikos Kyrpides, Natalia Ivanova:
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes. D560-D565 - Baofeng Jia, Amogelang R. Raphenya, Brian P. Alcock, Nicholas Waglechner, Peiyao Guo, Kara K. Tsang, Briony A. Lago, Biren M. Dave, Sheldon K. Pereira, Arjun N. Sharma, Sachin Doshi, Mélanie Courtot, Raymond Lo, Laura E. Williams, Jonathan G. Frye, Tariq Elsayegh, Daim Sardar, Erin L. Westman, Andrew C. Pawlowski, Timothy A. Johnson, Fiona S. L. Brinkman, Gerard D. Wright, Andrew G. McArthur:
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. D566-D573 - Steven M. Lakin, Christopher J. Dean, Noelle R. Noyes, Adam Dettenwanger, Anne Spencer Ross, Enrique Doster, Pablo Rovira, Zaid Abdo, Kenneth L. Jones, Jaime Ruiz, Keith E. Belk, Paul S. Morley, Christina Boucher:
MEGARes: an antimicrobial resistance database for high throughput sequencing. D574-D580 - Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C. Kissinger, Cris Lawrence, Wei Li, Deborah F. Pinney, Jane A. Pulman, David S. Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J. Stoeckert Jr., Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng:
EuPathDB: the eukaryotic pathogen genomics database resource. D581-D591 - Marek S. Skrzypek, Jonathan Binkley, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock:
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data. D592-D596 - Pedro Tiago Monteiro, Pedro Pais, Catarina Costa, Sauvagya Manna, Isabel Sá-Correia, Miguel Cacho Teixeira:
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts. D597-D603 - Martin Urban, Alayne Cuzick, Kim Rutherford, Alistair G. Irvine, Helder Pedro, Rashmi Pant, Vidyendra Sadanadan, Lokanath Khamari, Santoshkumar Billal, Sagar Mohanty, Kim E. Hammond-Kosack:
PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database. D604-D610 - Linhuan Wu, Qinglan Sun, Philippe Desmeth, Hideaki Sugawara, Zhenghong Xu, Kevin McCluskey, David Smith, Vasilenko Alexander, Nelson Lima, Moriya Ohkuma, Vincent Robert, Yuguang Zhou, Jianhui Li, Guomei Fan, Supawadee Ingsriswang, Svetlana Ozerskaya, Juncai Ma:
World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide. D611-D618
- Bethan Yates, Bryony Braschi, Kristian A. Gray, Ruth L. Seal, Susan Tweedie, Elspeth A. Bruford:
Genenames.org: the HGNC and VGNC resources in 2017. D619-D625 - Cath Tyner, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Christopher Eisenhart, Clayton M. Fischer, David Gibson, Jairo Navarro Gonzalez, Luvina Guruvadoo, Maximilian Haeussler, Steven G. Heitner, Angie S. Hinrichs, Donna Karolchik, Brian T. Lee, Christopher M. Lee, Parisa Nejad, Brian J. Raney, Kate R. Rosenbloom, Matthew L. Speir, Chris Villarreal, John Vivian, Ann S. Zweig, David Haussler, Michael Kuhn, W. James Kent:
The UCSC Genome Browser database: 2017 update. D626-D634 - Bronwen L. Aken, Premanand Achuthan, Wasiu A. Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla A. Cummins, Peter Clapham, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Thomas Juettemann, Stephen Keenan, Matthew R. Laird, Ilias Lavidas, Thomas Maurel, William M. McLaren, Benjamin Moore, Daniel N. Murphy, Rishi Nag, Victoria Newman, Michael Nuhn, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Steven P. Wilder, Amonida Zadissa, Myrto Kostadima, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Fiona Cunningham, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2017. D635-D642 - Yiming Lu, Cheng Quan, Hebing Chen, Xiaochen Bo, Chenggang Zhang:
3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes. D643-D649 - Daniel E. Cook, Stefan Zdraljevic, Joshua P. Roberts, Erik C. Andersen:
CeNDR, the Caenorhabditis elegans natural diversity resource. D650-D657 - Shenglin Mei, Qian Qin, Qiu Wu, Hanfei Sun, Rongbin Zheng, Chongzhi Zang, Muyuan Zhu, Jiaxin Wu, Xiaohui Shi, Len Taing, Tao Liu, Myles Brown, Clifford A. Meyer, Xiaole Shirley Liu:
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. D658-D662 - L. Sian Gramates, Steven J. Marygold, Gilberto dos Santos, Jose-Maria Urbano, Giulia Antonazzo, Beverley Matthews, Alix J. Rey, Christopher J. Tabone, Madeline A. Crosby, David B. Emmert, Kathleen Falls, Joshua L. Goodman, Yanhui Hu, Laura Ponting, Andrew J. Schroeder, Victor B. Strelets, Jim Thurmond, Pinglei Zhou, The FlyBase Consortium:
FlyBase at 25: looking to the future. D663-D671 - Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, Stephanie E. Mohr:
FlyRNAi.org - the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update. D672-D678 - Benedikt Rauscher, Florian Heigwer, Marco Breinig, Jan Winter, Michael Boutros:
GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens. D679-D686 - Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L. L. Sonnhammer:
HieranoiDB: a database of orthologs inferred by Hieranoid. D687-D690